The accumulation of over 11 million tons of spent lithium-ion batteries (LIBs) by 2030 highlights a critical environmental challenge posed by their large-scale retirement. The efficient recycling valuable metals from spent LIBs can both reduces environmental impact and mitigates the pressing issue of metal resource scarcity. In this context, deep eutectic solvents (DESs) have become a promising option as an eco-friendly solvent, exhibiting great potential for recycling spent LIBs. Therefore, this work proposed an innovative green DES system consisting of choline chloride (ChCl), DL-malic acid (MAL), and glycerol for the efficient leaching of valuable metals from spent LIBs. Comprehensive experiments were conducted to determine the optimum leaching conditions (130 °C, 60 g/L, MChCl:MAL:Glycerol of 1:1:3, 3 h), achieving high leaching efficiencies of 94.6% for Ni, 96.8% for Co, 93.8% for Mn, and 96.4% for Li. Through characterization techniques, kinetics studies, and density functional theory (DFT) calculations, the leaching process was predominantly governed by surface chemical reaction (1-(1-x)1/3 = kt) within the shrinking core model, exhibited activation energies of 49.89 kJ/mol, 47.66 kJ/mol, 50.51 kJ/mol, and 22.24 kJ/mol for Ni, Co, Mn, and Li, respectively. The propensity for DES to leach metal ions followed the order: Li > Co > Ni > Mn, determined by binding energy and energy gaps. Cl− and −COOH within the DES were capable of forming stable complexes with reduced transition metal ions, revealing an efficient coordination leaching mechanism. Additionally, a life cycle assessment (LCA) was conducted on the environmental impacts of the DES leaching process, confirming it as an effective and environmentally friendly method for recycling spent LIBs. This work avoided the employment of corrosive acids and alleviated the generally harsh conditions associated with DESs leaching, providing a viable solution for recovering spent LIBs.